sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.830 Å
X-ray
2012-06-27
| Name: | Beta-secretase 1 |
|---|---|
| ID: | BACE1_HUMAN |
| AC: | P56817 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.4.23.46 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 20.628 |
|---|---|
| Number of residues: | 45 |
| Including | |
| Standard Amino Acids: | 44 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.857 | 1019.250 |
| % Hydrophobic | % Polar |
|---|---|
| 29.47 | 70.53 |
| According to VolSite | |
| HET Code: | I6X |
|---|---|
| Formula: | C30H26FN4O |
| Molecular weight: | 477.552 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.1 % |
| Polar Surface area: | 73.19 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 5.42881 | 1.76 | -20.5678 |
Image generated by PoseView
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
| Ligand | Protein | Interaction | |||
|---|---|---|---|---|---|
| Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
| C34 | CD1 | LEU- 30 | 4.42 | 0 | Hydrophobic |
| C29 | CD2 | LEU- 30 | 3.83 | 0 | Hydrophobic |
| N20 | OD1 | ASP- 32 | 2.9 | 168.87 | H-Bond (Ligand Donor) |
| C10 | CB | SER- 35 | 3.96 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 69 | 3.86 | 0 | Hydrophobic |
| C2 | CD1 | TYR- 71 | 3.64 | 0 | Hydrophobic |
| O9 | NE1 | TRP- 76 | 2.84 | 164.2 | H-Bond (Protein Donor) |
| C10 | CE1 | PHE- 108 | 4.27 | 0 | Hydrophobic |
| C10 | CG2 | ILE- 118 | 4.02 | 0 | Hydrophobic |
| C24 | CD1 | ILE- 118 | 3.54 | 0 | Hydrophobic |
| N20 | OD2 | ASP- 228 | 2.94 | 152.34 | H-Bond (Ligand Donor) |
| F21 | CB | THR- 231 | 4.38 | 0 | Hydrophobic |
| C36 | CB | ALA- 335 | 3.48 | 0 | Hydrophobic |
